In our installation of Fogbugz, we have a long list of projects (and it's been growing). The projects are easily split up between teams. So most developers only really care about the couple projects his team is working on. It would be nice to be able to have another level of hierarchy above "Project" that would allow the projects to be sorted and more easily according to each functional group (acting similar to the "Project"/"Area" relationship).
One of our users actually wrote a plugin that implements this feature. It needed to be a little hacky though to get the new drop-down menu to display in the right spot (left of the "Project" drop-down). The other problem is maintainability. Our plugin has to be fixed over and over as Fogbugz grows and changes from release to release. It might be nice to add support for gui manipulation to the api if you can't add this kind of functionality as a core feature.
What we have right now is a new "Organization" drop-down that filters the next "Project" drop-down (only displays projects in the selected organization). The "Project drop-down then filters the "Area" drop-down as it does in the normal installation.